The thermal behavior of luciferase on nanofabricated hydrophilic Si surface was investigated using molecular dynamics simulations. At high temperature, LUC_CHANGES (structural changes in the active site of luciferase) were smaller on the nanofabricated hydrophilic Si surface than on a non-nanofabricated hydrophilic Si surface, although LUC_CHANGES were slightly larger on the nanofabricated hydrophilic Si surface than on a non-nanofabricated hydrophobic Si surface. At room temperature, LUC_CHANGES were smaller on the nanofabricated hydrophilic Si surface than on a non-nanofabricated and wet-treated Si surface. Thus, nanofabricated hydrophilic Si surface would be preferable for practical applications.